Target Identification for Small Bioactive Molecules: Finding the Needle in the Haystack

Identification and confirmation of bioactive small‐molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state‐of‐the‐art. Among the techniques currently available, protein affinity isolation using suitable small‐molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins.     

On a property of polyhedral sets

The following result is proved using solvability and optimality criteria for linear programs. The duals to the cones of feasible directions at vertices of a polyhedral set constitute a partition of the dual to the recession cone of the set.     

Chemical Genetics Reveals a Role of dCTP Pyrophosphatase 1 in Wnt Signaling

Cell‐based screening is a powerful approach to identify novel chemical modulators and biological components of relevant biological processes. The canonical Wnt pathway is essential for normal embryonic development and tissue homeostasis, and its deregulation plays a crucial role in carcinogenesis. Therefore, the identification of new pathway members and regulators is of significant interest. By means of a cell‐based assay monitoring Wnt signaling we identified the pyrrolocoumarin Pyrcoumin as inhibitor of canonical Wnt signaling. Target identification and validation revealed that Pyrcoumin is a competitive inhibitor of dCTP pyrophosphatase 1 (dCTPP1). We demonstrate a yet unknown interaction of dCTPP1 with ubiquitin carboxyl‐terminal hydrolase (USP7) that is counteracted by dCTPP1 inhibitors. These findings indicate that dCTPP1 plays a role in regulation of Wnt/β‐catenin signaling most likely through a direct interaction with USP7.     

A new solution for dilaton-Maxwell gravity

An interesting static spherically symmetric solution corresponding to Einstein-Maxwell gravity coupled to a dilaton field with negative kinetic term has been obtained. This solution is characterized by the set of two arbitrary parameters, the physical mass ₀ and electric chargeQ. It has two horizons on which the metric, scalar curvature and both dilaton and electromagnetic fields are regular. Another feature of this solution is that the physical mass is bounded by the electric charge as ₀2¦Q¦ (unlike the Reisner-Nordström solution for which ₀>-¦Q¦). The structure of the scalar curvature has been analyzed.On leave from: Bogolyubov Institute for Theoretical Microphysics, Moscow State University, 119899 Moscow, Russia     

Unravelling the Synthesis and Chemistry of Stable,Acyclic, and Double-Deficient 1,3-Butadienes: An endo-Selective Diels–Alder Route to Hedgehog Pathway Inhibitors

The first synthetic access to stable and acyclic 1,3-butadienes with two electron-withdrawing carbonyl groups and their potential to deliver new molecular scaffolds through intriguing endo-selective Diels–Alder cycloadditions are presented. The bicyclic scaffolds produced through the cycloaddition chemistry of electron-deficient dienes afforded potent Hedgehog signaling pathway inhibitors.     

A Scaffold-Diversity Synthesis of Biologically Intriguing Cyclic Sulfonamides

A “branching–folding” synthetic strategy that affords a range of diverse cyclic benzo-sulfonamide scaffolds is presented. Whereas different annulation reactions on common ketimine substrates build the branching phase of the scaffold synthesis, a common hydrogenative ring-expansion method, facilitated by an increase of the ring-strain during the branching phase, led to sulfonamides bearing medium-sized rings in a folding pathway. Cell painting assay was successfully employed to identify tubulin targeting sulfonamides as novel mitotic inhibitors.     

Symmetry breaking in an initially curved micro beam loaded by a distributed electrostatic force

The asymmetric buckling of a shallow initially curved stress-free micro beam subjected to distributed nonlinear deflection-dependent electrostatic force is studied. In order to highlight the symmetry breaking phenomenon and the approach to its analysis, the subsidiary simplified problem of a curved beam attached to a linearly elastic foundation, and subjected to uniformly distributed “mechanical” load, which is independent of deflections, is addressed first. The analysis is based on a two degrees of freedom reduced order (RO) model resulting from the Galerkin decomposition with linear undamped eigenmodes of a straight beam used as the base functions. Simple approximate expressions are derived defining the geometric parameters of beams for which an asymmetric response bifurcates from the symmetric one. The necessary criterion establishes the conditions for the appearance of bifurcation points on the unstable branch of the symmetric limit point buckling curve; the sufficient criterion assures a realistic asymmetric buckling bifurcating from the stable branches of the curve. It is shown that while the symmetry breaking conditions are affected by the nonlinearity of the electrostatic force, its influence is less pronounced than in the case of the symmetric snap-through criterion. A comparison between the RO model results and those obtained by direct numerical analysis shows good agreement between the two and indicates that the obtained criteria can be used to predict non-symmetric buckling in electrostatically actuated bistable micro beams.     

Unprecedented Combination of Polyketide Natural Product Fragments Identifies the New Hedgehog Signaling Pathway Inhibitor Grismonone

Pseudo-natural products (pseudo-NPs) are de novo combinations of natural product (NP) fragments that define novel bioactive chemotypes. For their discovery, new design principles are being sought. Previously, pseudo-NPs were synthesized by the combination of fragments originating from biosynthetically unrelated NPs to guarantee structural novelty and novel bioactivity. We report the combination of fragments from biosynthetically related NPs in novel arrangements to yield a novel chemotype with activity not shared by the guiding fragments. We describe the synthesis of the polyketide pseudo-NP grismonone and identify it as a structurally novel and potent inhibitor of Hedgehog signaling. The insight that the de novo combination of fragments derived from biosynthetically related NPs may also yield new biologically relevant compound classes with unexpected bioactivity may be considered a chemical extension or diversion of existing biosynthetic pathways and greatly expands the opportunities for exploration of biologically relevant chemical space by means of the pseudo-NP principle.